PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM > Class Template Reference
#include <PseudoEcgCalculator.hpp>
Public Member Functions | |
| PseudoEcgCalculator (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, const ChastePoint< SPACE_DIM > &rProbeElectrode, std::string directory, std::string hdf5File, std::string variableName="V", bool makeAbsolute=true) | |
| ~PseudoEcgCalculator () | |
| void | SetDiffusionCoefficient (double diffusionCoefficient) |
| void | WritePseudoEcg () |
Private Member Functions | |
| double | GetIntegrand (ChastePoint< SPACE_DIM > &rX, c_vector< double, PROBLEM_DIM > &rU, c_matrix< double, PROBLEM_DIM, SPACE_DIM > &rGradU) |
| double | ComputePseudoEcgAtOneTimeStep (unsigned timeStep) |
Private Attributes | |
| Hdf5DataReader * | mpDataReader |
| unsigned | mNumberOfNodes |
| unsigned | mNumTimeSteps |
| AbstractTetrahedralMesh < ELEMENT_DIM, SPACE_DIM > & | mrMesh |
| ChastePoint< SPACE_DIM > | mProbeElectrode |
| double | mDiffusionCoefficient |
| std::string | mVariableName |
Friends | |
| class | TestPseudoEcgCalculator |
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM, unsigned PROBLEM_DIM>
class PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >
This class implements a pseudo-ECG calculator. It is a concrete class of AbstractFunctionalCalculator. The pseudo-ECG is defined as the integral over the mesh of the following integrand:
- D * grad (solution) dot grad (1/r)
where D is a diffusion coefficient and r is the distance between a recording electrode and a given point in the mesh.
References for the formula that defines the pseudo-ECG:
Gima K, Rudy Y Circ Res (2002) 90:889-896 (equation 1) Baher et al. Am J Physiol (2007) 292:H180-H189 (equation 5)
Definition at line 54 of file PseudoEcgCalculator.hpp.
Constructor & Destructor Documentation
| PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator | ( | AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & | rMesh, | |
| const ChastePoint< SPACE_DIM > & | rProbeElectrode, | |||
| std::string | directory, | |||
| std::string | hdf5File, | |||
| std::string | variableName = "V", |
|||
| bool | makeAbsolute = true | |||
| ) | [inline] |
Constructor
- Parameters:
-
rMesh A reference to the mesh rProbeElectrode The location of the recording electrode directory The directory where the simulation results are stored hdf5File The file name where the simulation results are stored variableName The name of the voltage variable (hardcoded to V - see todo) makeAbsolute whether to make the path of directory absolute (using the OutputFileHandler)
Definition at line 54 of file PseudoEcgCalculator.cpp.
References Hdf5DataReader::GetNumberOfRows(), Hdf5DataReader::GetVariableOverTime(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumberOfNodes, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumTimeSteps, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mrMesh, and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName.
| PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~PseudoEcgCalculator | ( | ) | [inline] |
Destructor.
Definition at line 75 of file PseudoEcgCalculator.cpp.
References PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader.
Member Function Documentation
| double PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetIntegrand | ( | ChastePoint< SPACE_DIM > & | rX, | |
| c_vector< double, PROBLEM_DIM > & | rU, | |||
| c_matrix< double, PROBLEM_DIM, SPACE_DIM > & | rGradU | |||
| ) | [inline, private, virtual] |
Get the integrand. The pseudo-ECG is defined as the integral over the mesh of the following integrand:
- D * grad (solution) dot grad (1/r)
- Parameters:
-
rX The point in space rU The unknown as a vector, u(i) = u_i rGradU The gradient of the unknown as a matrix, rGradU(i,j) = d(u_i)/d(X_j)
Implements AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >.
Definition at line 36 of file PseudoEcgCalculator.cpp.
References EXCEPTION, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mProbeElectrode, and ChastePoint< DIM >::rGetLocation().
| double PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep | ( | unsigned | timeStep | ) | [inline, private] |
Calculates the pseudo-ECG and returns its value at the given time step.
- Parameters:
-
timeStep the time step where we want to calculate the pseudoecg
- Returns:
- the pseudo ECG at the given time step.
Definition at line 88 of file PseudoEcgCalculator.cpp.
References AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), PetscTools::CreateVec(), Hdf5DataReader::GetVariableOverNodes(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumberOfNodes, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader, PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mrMesh, and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().
| void PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetDiffusionCoefficient | ( | double | diffusionCoefficient | ) | [inline] |
Sets the value of the diffusion coefficient (D)
- Parameters:
-
diffusionCoefficient The desired value of the diffusion coefficient
Definition at line 81 of file PseudoEcgCalculator.cpp.
References PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient.
| void PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg | ( | ) | [inline] |
Calculates and writes the pseudo-ECG to file. the file will be named PseudoEcg.dat. It will contain one column of numbers, each being the pseudoECG at each time step. It will be created by the master processor into /output relaitive to where the output directory is set (by the HeartConfig or by default)
Definition at line 108 of file PseudoEcgCalculator.cpp.
References PetscTools::AmMaster(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), ChasteBuildInfo::GetProvenanceString(), HeartConfig::Instance(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumTimeSteps, and OutputFileHandler::OpenOutputFile().
Member Data Documentation
Hdf5DataReader* PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mpDataReader [private] |
An HDF5 reader from which to get the solution
Definition at line 60 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::~PseudoEcgCalculator().
unsigned PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumberOfNodes [private] |
Number of nodes in the mesh (got from the data reader)
Definition at line 61 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().
unsigned PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mNumTimeSteps [private] |
Number of time steps in the simulation (got from the data reader)
Definition at line 62 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WritePseudoEcg().
AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mrMesh [private] |
A mesh used by the calculator
Definition at line 63 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().
ChastePoint<SPACE_DIM> PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mProbeElectrode [private] |
The point from where we want to calculate the pseudoECG
Definition at line 64 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetIntegrand().
double PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mDiffusionCoefficient [private] |
The diffusion coefficient D
Definition at line 65 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetIntegrand(), PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::SetDiffusionCoefficient().
std::string PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::mVariableName [private] |
the variable for which we want to calculate the pseudo ecg, defaults to "V"
Definition at line 66 of file PseudoEcgCalculator.hpp.
Referenced by PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputePseudoEcgAtOneTimeStep(), and PseudoEcgCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::PseudoEcgCalculator().
The documentation for this class was generated from the following files:
- heart/src/postprocessing/PseudoEcgCalculator.hpp
- heart/src/postprocessing/PseudoEcgCalculator.cpp
